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vtraag / leidenalg

Implementation of the Leiden algorithm for various quality functions to be used with igraph in Python.
GNU General Public License v3.0
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Could not construct partition: vector #117

Closed AlduCor closed 1 year ago

AlduCor commented 1 year ago

Hi I've recently upgraded from python-igraph 0.9 to igraph 0.10 since python-igraph seems is superceded by igraph (see: https://pypi.org/project/python-igraph/). I'm on MacOS, using conda.

However, when I run the following my get an error:

import leidenalg
import igraph as ig
G = ig.Graph.Famous('Zachary')
leidenalg.find_partition(G, leidenalg.ModularityVertexPartition)

Error Trace

---------------------------------------------------------------------------
BaseException                             Traceback (most recent call last)
/...02_mm_graphs.ipynb Cell 16 in <cell line: 4>()
      2 import igraph as ig
      3 G = ig.Graph.Famous('Zachary')
----> 4 leidenalg.find_partition(G, leidenalg.ModularityVertexPartition)

File ~/miniforge3/envs/.../lib/python3.9/site-packages/leidenalg/functions.py:81, in find_partition(graph, partition_type, initial_membership, weights, n_iterations, max_comm_size, seed, **kwargs)
     79 if not weights is None:
     80   kwargs['weights'] = weights
---> 81 partition = partition_type(graph,
     82                            initial_membership=initial_membership,
     83                            **kwargs)
     84 optimiser = Optimiser()
     86 optimiser.max_comm_size = max_comm_size

File ~/miniforge3/envs/.../lib/python3.9/site-packages/leidenalg/VertexPartition.py:456, in ModularityVertexPartition.__init__(self, graph, initial_membership, weights)
    452   else:
    453     # Make sure it is a list
    454     weights = list(weights)
--> 456 self._partition = _c_leiden._new_ModularityVertexPartition(pygraph_t,
    457     initial_membership, weights)
    458 self._update_internal_membership()

BaseException: Could not construct partition: vector

My Conda env

> conda list
# packages in environment at /.venv:
#
# Name                    Version                   Build  Channel
anyio                     3.6.2              pyhd8ed1ab_0    conda-forge
appnope                   0.1.3              pyhd8ed1ab_0    conda-forge
argon2-cffi               21.3.0             pyhd8ed1ab_0    conda-forge
argon2-cffi-bindings      21.2.0           py39h02fc5c5_3    conda-forge
asttokens                 2.1.0              pyhd8ed1ab_0    conda-forge
attrs                     22.1.0             pyh71513ae_1    conda-forge
backcall                  0.2.0              pyh9f0ad1d_0    conda-forge
backports                 1.0                        py_2    conda-forge
backports.functools_lru_cache 1.6.4              pyhd8ed1ab_0    conda-forge
beautifulsoup4            4.11.1             pyha770c72_0    conda-forge
bleach                    5.0.1              pyhd8ed1ab_0    conda-forge
bzip2                     1.0.8                h3422bc3_4    conda-forge
ca-certificates           2022.9.24            h4653dfc_0    conda-forge
certifi                   2022.9.24                pypi_0    pypi
cffi                      1.15.1           py39h7e6b969_1    conda-forge
charset-normalizer        2.1.1                    pypi_0    pypi
contourpy                 1.0.6                    pypi_0    pypi
cycler                    0.11.0                   pypi_0    pypi
debugpy                   1.6.3            py39h23fbdae_1    conda-forge
decorator                 5.1.1              pyhd8ed1ab_0    conda-forge
defusedxml                0.7.1              pyhd8ed1ab_0    conda-forge
entrypoints               0.4                pyhd8ed1ab_0    conda-forge
executing                 1.2.0              pyhd8ed1ab_0    conda-forge
flit-core                 3.8.0              pyhd8ed1ab_0    conda-forge
fonttools                 4.38.0                   pypi_0    pypi
idna                      3.4                pyhd8ed1ab_0    conda-forge
igraph                    0.10.2                   pypi_0    pypi
importlib-metadata        5.0.0              pyha770c72_1    conda-forge
importlib_resources       5.10.0             pyhd8ed1ab_0    conda-forge
ipykernel                 6.17.0             pyh736e0ef_0    conda-forge
ipython                   8.6.0              pyhd1c38e8_1    conda-forge
ipython_genutils          0.2.0                      py_1    conda-forge
ipywidgets                8.0.2              pyhd8ed1ab_1    conda-forge
jedi                      0.18.1             pyhd8ed1ab_2    conda-forge
jinja2                    3.1.2              pyhd8ed1ab_1    conda-forge
jsonschema                4.17.0             pyhd8ed1ab_0    conda-forge
jupyter                   1.0.0            py39h2804cbe_7    conda-forge
jupyter_client            7.4.4              pyhd8ed1ab_0    conda-forge
jupyter_console           6.4.4              pyhd8ed1ab_0    conda-forge
jupyter_core              4.11.2           py39h2804cbe_0    conda-forge
jupyter_server            1.21.0             pyhd8ed1ab_0    conda-forge
jupyterlab_pygments       0.2.2              pyhd8ed1ab_0    conda-forge
jupyterlab_widgets        3.0.3              pyhd8ed1ab_0    conda-forge
kiwisolver                1.4.4                    pypi_0    pypi
leidenalg                 0.9.0                    pypi_0    pypi
libblas                   3.9.0           16_osxarm64_openblas    conda-forge
libcblas                  3.9.0           16_osxarm64_openblas    conda-forge
libcxx                    14.0.6               h2692d47_0    conda-forge
libffi                    3.4.2                h3422bc3_5    conda-forge
libgfortran               5.0.0           11_3_0_hd922786_25    conda-forge
libgfortran5              11.3.0              hdaf2cc0_25    conda-forge
liblapack                 3.9.0           16_osxarm64_openblas    conda-forge
libopenblas               0.3.21          openmp_hc731615_3    conda-forge
libsodium                 1.0.18               h27ca646_1    conda-forge
libsqlite                 3.39.4               h76d750c_0    conda-forge
libzlib                   1.2.13               h03a7124_4    conda-forge
llvm-openmp               14.0.4               hd125106_0    conda-forge
markupsafe                2.1.1            py39h02fc5c5_2    conda-forge
matplotlib                3.6.2                    pypi_0    pypi
matplotlib-inline         0.1.6              pyhd8ed1ab_0    conda-forge
mistune                   2.0.4              pyhd8ed1ab_0    conda-forge
nbclassic                 0.4.8              pyhd8ed1ab_0    conda-forge
nbclient                  0.7.0              pyhd8ed1ab_0    conda-forge
nbconvert                 7.2.3              pyhd8ed1ab_0    conda-forge
nbconvert-core            7.2.3              pyhd8ed1ab_0    conda-forge
nbconvert-pandoc          7.2.3              pyhd8ed1ab_0    conda-forge
nbformat                  5.7.0              pyhd8ed1ab_0    conda-forge
ncurses                   6.3                  h07bb92c_1    conda-forge
nest-asyncio              1.5.6              pyhd8ed1ab_0    conda-forge
networkx                  2.8.8                    pypi_0    pypi
notebook                  6.5.2              pyha770c72_1    conda-forge
notebook-shim             0.2.2              pyhd8ed1ab_0    conda-forge
numpy                     1.23.4           py39hefdcf20_1    conda-forge
openssl                   3.0.7                h03a7124_0    conda-forge
packaging                 21.3               pyhd8ed1ab_0    conda-forge
pandas                    1.5.1            py39hde7b980_1    conda-forge
pandoc                    2.19.2               hce30654_1    conda-forge
pandocfilters             1.5.0              pyhd8ed1ab_0    conda-forge
parso                     0.8.3              pyhd8ed1ab_0    conda-forge
pexpect                   4.8.0              pyh1a96a4e_2    conda-forge
pickleshare               0.7.5                   py_1003    conda-forge
pillow                    9.3.0                    pypi_0    pypi
pip                       22.3.1             pyhd8ed1ab_0    conda-forge
pkgutil-resolve-name      1.3.10             pyhd8ed1ab_0    conda-forge
prometheus_client         0.15.0             pyhd8ed1ab_0    conda-forge
prompt-toolkit            3.0.32             pyha770c72_0    conda-forge
prompt_toolkit            3.0.32               hd8ed1ab_0    conda-forge
psutil                    5.9.3            py39h02fc5c5_1    conda-forge
ptyprocess                0.7.0              pyhd3deb0d_0    conda-forge
pure_eval                 0.2.2              pyhd8ed1ab_0    conda-forge
pycairo                   1.21.0                   pypi_0    pypi
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pygments                  2.13.0             pyhd8ed1ab_0    conda-forge
pyparsing                 3.0.9              pyhd8ed1ab_0    conda-forge
pyrsistent                0.19.2           py39h02fc5c5_0    conda-forge
python                    3.9.13          h96fcbfb_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-dotenv             0.21.0                   pypi_0    pypi
python-fastjsonschema     2.16.2             pyhd8ed1ab_0    conda-forge
python_abi                3.9                      2_cp39    conda-forge
pytz                      2022.6             pyhd8ed1ab_0    conda-forge
pyzmq                     24.0.1           py39h0553236_1    conda-forge
readline                  8.1.2                h46ed386_0    conda-forge
requests                  2.28.1                   pypi_0    pypi
scipy                     1.9.3                    pypi_0    pypi
send2trash                1.8.0              pyhd8ed1ab_0    conda-forge
setuptools                65.5.1             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sniffio                   1.3.0              pyhd8ed1ab_0    conda-forge
soupsieve                 2.3.2.post1        pyhd8ed1ab_0    conda-forge
sqlite                    3.39.4               h2229b38_0    conda-forge
stack_data                0.6.0              pyhd8ed1ab_0    conda-forge
terminado                 0.17.0             pyhd1c38e8_0    conda-forge
texttable                 1.6.4                    pypi_0    pypi
tinycss2                  1.2.1              pyhd8ed1ab_0    conda-forge
tk                        8.6.12               he1e0b03_0    conda-forge
tornado                   6.2              py39h02fc5c5_1    conda-forge
tqdm                      4.64.1                   pypi_0    pypi
traitlets                 5.5.0              pyhd8ed1ab_0    conda-forge
trieregex                 1.0.0                    pypi_0    pypi
typing_extensions         4.4.0              pyha770c72_0    conda-forge
tzdata                    2022f                h191b570_0    conda-forge
ujson                     5.5.0                    pypi_0    pypi
urllib3                   1.26.12                  pypi_0    pypi
vadersentiment            3.3.2                    pypi_0    pypi
wcwidth                   0.2.5              pyh9f0ad1d_2    conda-forge
webencodings              0.5.1                      py_1    conda-forge
websocket-client          1.4.2              pyhd8ed1ab_0    conda-forge
wheel                     0.38.2             pyhd8ed1ab_0    conda-forge
widgetsnbextension        4.0.3              pyhd8ed1ab_0    conda-forge
xlrd                      2.0.1                    pypi_0    pypi
xlsxwriter                3.0.3                    pypi_0    pypi
xz                        5.2.6                h57fd34a_0    conda-forge
zeromq                    4.3.4                hbdafb3b_1    conda-forge
zipp                      3.10.0             pyhd8ed1ab_0    conda-forge
AlduCor commented 1 year ago

You can safely ignore me. For posterity, the version of leidenalg and igraph were not in sync, due to pebkac.